Resolving deep animal phylogeny with irreversible and unrepeatable genomic changes

通过不可逆和不可重复的基因组变化解决深层动物系统发育

• 批准号: EP/Y023668/1
• 负责人: Maximilian Telford
• 金额: $ 25.55万
• 依托单位: University College London
• 依托单位国家: 英国
• 项目类别: Fellowship
• 财政年份: 2024
• 资助国家: 英国
• 起止时间: 2024 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=EP%2FY023668%2F1
• 关键词: Resolving; deep; animal; phylogeny; irreversible

Resolving the animal tree of life is essential to understand the origin and evolution of complex traits such as muscles, guts, and a nervous system. Sequence-based phylogenomics has not met expectations- replacing old problems in animal phylogenetics with new ones. Different datasets and phylogenetic models routinely produce strongly supported but incompatible trees. A key driver of this is convergent evolution of the same nucleotide or amino acid character state at a given position in distantly related sequences by reverse or parallel substitutions. This is prevalent, given the few possible alternative nucleotide (4) or amino acid (20) states, and can produce incorrect trees. Despite substantial effort, adequate and tractable solutions to this and related problems continue to evade us, confounding understanding of animal evolution. An alternative is rare genomic changes, e.g. presence/absence of genes, indels, introns, gene clusters, protein domain architecture etc. Such complex characters are very unlikely to have evolved convergently and their presence/absence is a binary character uniting species. Despite the potential and growing use of such methods, it is already clear that like phylogenomics, they can be misled; character loss can be convergent and is indistinguishable from primary absence. To circumvent this, we will build computational tools for systematic genome-wide identification of a special class of rare genomic changes that employ 'irreversible', 'unrepeatable' characters. These characters are never absent and take two equally and highly complex conserved states-one ancestral (present in non-animals and some animals) and one derived (present in the remaining animals)-making reverse or parallel evolution vanishingly unlikely (e.g. gene adjacency relationships, 'conserved-but-different' genes). This will produce a new, confidently-resolved animal phylogeny allowing us to trace the history of animal trait evolution in ancient Precambrian oceans.

解析动物生命树对于理解肌肉、内脏和神经系统等复杂特征的起源和进化至关重要。以序列为基础的基因组学并没有达到人们的期望--用新的问题取代动物基因组学中的旧问题。不同的数据集和系统发育模型通常会产生强支持但不兼容的树。其关键驱动力是通过反向或平行取代在远缘相关序列中的给定位置处的相同核苷酸或氨基酸特征状态的趋同进化。这是普遍的，考虑到很少可能的替代核苷酸（4）或氨基酸（20）状态，并且可以产生不正确的树。尽管我们付出了巨大的努力，但我们仍然无法找到解决这个问题和相关问题的适当和易处理的方法，这混淆了我们对动物进化的理解。另一种选择是罕见的基因组变化，例如基因，插入缺失，内含子，基因簇，蛋白质结构域架构等的存在/不存在。这种复杂的字符是非常不可能进化收敛和他们的存在/不存在是一个二元字符团结物种。尽管这些方法有潜力，而且越来越多地被使用，但已经很清楚，它们可能会被误导;性格丧失可能是趋同的，与原发性缺失无法区分。为了规避这一点，我们将建立计算工具，系统的全基因组识别一类特殊的罕见的基因组变化，采用“不可逆的”，“不可重复的”字符。这些特征从不缺席，并采取两种同等和高度复杂的保守状态-一种是祖先的（存在于非动物和一些动物中），一种是衍生的（存在于其余动物中）-使反向或平行进化几乎不可能（例如基因邻接关系，“保守但不同”的基因）。这将产生一个新的，有信心解决的动物遗传学，使我们能够追溯古代前寒武纪海洋中动物性状进化的历史。